85 lines
2.6 KiB
Ruby
85 lines
2.6 KiB
Ruby
class Blast < Formula
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desc "Basic Local Alignment Search Tool"
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homepage "https://blast.ncbi.nlm.nih.gov/"
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url "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-src.tar.gz"
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version "2.13.0"
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sha256 "89553714d133daf28c477f83d333794b3c62e4148408c072a1b4620e5ec4feb2"
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license :public_domain
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livecheck do
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url "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/VERSION"
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regex(/v?(\d+(?:\.\d+)+)/i)
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end
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bottle do
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rebuild 1
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sha256 arm64_big_sur: "78881b3e87d3fb5d3fa1aef2a25d8390097432de3a5d10521ca5fb4e7ca56496"
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sha256 monterey: "e144139a12c6f56996071cb3efcb57b552f937d0dfef61d577f12f9436cf8775"
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sha256 big_sur: "9d406671f65bb9271f1564d6dcd3dcb7adfda11304c856632c30338b282e5891"
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sha256 catalina: "9e06f6116d53ee375d166487ffa8dff40a7083dc2fdc70e4f4f2b9a49e96ca11"
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sha256 x86_64_linux: "3313233f45a9a7cdde4867c98404ea0bf5b10f7827a188b935599a24885a01e1"
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end
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depends_on "lmdb"
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uses_from_macos "cpio" => :build
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uses_from_macos "bzip2"
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uses_from_macos "zlib"
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on_macos do
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depends_on "libomp"
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end
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conflicts_with "proj", because: "both install a `libproj.a` library"
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fails_with gcc: "5" # C++17
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def install
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cd "c++" do
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# Boost is only used for unit tests.
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args = %W[
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--prefix=#{prefix}
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--with-bin-release
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--with-mt
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--with-strip
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--with-experimental=Int8GI
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--without-debug
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--without-boost
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]
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# Allow SSE4.2 on some platforms. The --with-bin-release sets --without-sse42
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args << "--with-sse42" if Hardware::CPU.intel? && MacOS.version.requires_sse42?
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if OS.mac?
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args += ["OPENMP_FLAGS=-Xpreprocessor -fopenmp",
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"LDFLAGS=-lomp"]
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end
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system "./configure", *args
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# Fix the error: install: ReleaseMT/lib/*.*: No such file or directory
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system "make"
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system "make", "install"
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end
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end
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test do
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output = shell_output("#{bin}/update_blastdb.pl --showall")
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assert_match "nt", output
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(testpath/"test.fasta").write <<~EOS
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>U00096.2:1-70
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AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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EOS
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output = shell_output("#{bin}/blastn -query test.fasta -subject test.fasta")
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assert_match "Identities = 70/70", output
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# Create BLAST database
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output = shell_output("#{bin}/makeblastdb -in test.fasta -out testdb -dbtype nucl")
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assert_match "Adding sequences from FASTA", output
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# Check newly created BLAST database
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output = shell_output("#{bin}/blastdbcmd -info -db testdb")
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assert_match "Database: test", output
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end
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end
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